PharmacoGx

DOI: 10.18129/B9.bioc.PharmacoGx    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see PharmacoGx.

Analysis of Large-Scale Pharmacogenomic Data

Bioconductor version: 3.13

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

Author: Petr Smirnov [aut], Zhaleh Safikhani [aut], Christopher Eeles [aut], Mark Freeman [aut], Benjamin Haibe-Kains [aut, cre]

Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains at utoronto.ca>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PharmacoGx")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("PharmacoGx")

 

PDF	R Script	Creating a PharmacoSet Object
PDF	R Script	PharmacoGx: An R Package for Analysis of Large Pharmacogenomic Datasets
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software
Version	2.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (5 years)
License	Artistic-2.0
Depends	R (>= 3.6), CoreGx
Imports	BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, glue
LinkingTo
Suggests	pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/bhklab/PharmacoGx/issues
Depends On Me
Imports Me	Xeva
Suggests Me	ToxicoGx
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	PharmacoGx_2.4.0.tar.gz
Windows Binary	PharmacoGx_2.4.0.zip
macOS 10.13 (High Sierra)	PharmacoGx_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PharmacoGx
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PharmacoGx
Package Short Url	https://bioconductor.org/packages/PharmacoGx/
Package Downloads Report	Download Stats